[Bioperl-l] Re peatMasker not found

vdar at yorku.ca vdar at yorku.ca
Thu May 22 14:55:48 EDT 2008


I can see that RepeatMasker program is there in this directory
/home/vdar/RepeatMasker

Here is a whole list of whats inside this directory

[vdar at capsella RepeatMasker]$ ls -al
total 35048
drwxr-xr-x   5 vdar users     4096 May 22 11:41 .
drwx------  10 vdar users     4096 May 22 14:15 ..
-rwxr-xr-x   1 vdar users    11386 May 20 14:26 ArrayListIterator.pm
-rwxr-xr-x   1 vdar users    13888 May 20 14:26 ArrayList.pm
-rw-r--r--   1 vdar users     1683 May 20 14:26 bluegrad.jpg
-rwxr-xr-x   1 vdar users    16439 May 20 14:26 configure
-rwxr-xr-x   1 vdar users    26098 May 20 14:26 CrossmatchSearchEngine.pm
-rwxr-xr-x   1 vdar users    26342 May 20 14:26 DateRepeats
-rw-r--r--   1 vdar users     5935 May 20 14:26 daterepeats.help
-rwxr-xr-x   1 vdar users    33871 May 20 14:26 DeCypherSearchEngine.pm
-rwxr-xr-x   1 vdar users    33265 May 20 14:26 DupMasker
-rwxr-xr-x   1 vdar users    54550 May 20 14:26 FastaDB.pm
-rw-r--r--   1 vdar users     6966 May 20 14:26 HTMLAnnotHeader.html
-rwxr--r--   1 vdar users     2543 May 20 14:26 INSTALL
drwxr-xr-x   2 vdar users     4096 May 20 14:26 Libraries
-rw-r--r--   1 vdar users     9862 May 20 14:26 license.txt
-rwxr-xr-x   1 vdar users   425419 May 20 14:26 LineHash.pm
drwxr-xr-x   4 vdar users     4096 May 20 14:26 Matrices
-rwxr-xr-x   1 vdar users   322391 May 20 14:26 ProcessRepeats
-rwxr-xr-x   1 vdar users     9381 May 20 14:26 PubRef.pm
-rwxr--r--   1 vdar users     1836 May 20 14:26 README
-rwxr-xr-x   1 vdar users    22385 May 20 14:26 RepbaseEMBL.pm
-rwxr-xr-x   1 vdar users    49282 May 20 14:26 RepbaseRecord.pm
-rwxr-xr-x   1 vdar users  3929708 May 20 14:26 RepeatAnnotationData.pm
-rwxr-xr-x   1 vdar users   213727 May 20 14:26 RepeatMasker
-rw-r--r--   1 vdar users     5721 May 20 14:26 RepeatMaskerConfig.pm
-rwxr-xr-x   1 vdar users     5689 May 20 14:26 RepeatMaskerConfig.tmpl
-rw-r--r--   1 vdar users    85557 May 20 14:26 repeatmasker.help
-rwxr-xr-x   1 vdar users    19538 May 20 14:26 RepeatProteinMask
-rwxr-xr-x   1 vdar users    17666 May 20 14:26 SearchEngineI.pm
-rwxr-xr-x   1 vdar users    24600 May 20 14:26 SearchResultCollection.pm
-rwxr-xr-x   1 vdar users    35040 May 20 14:26 SearchResult.pm
-rwxr-xr-x   1 vdar users    11565 May 20 14:26 SeqDBI.pm
-rwxr-xr-x   1 vdar users    25427 May 20 14:26 SimpleBatcher.pm
-rwxr--r--   1 vdar users 30140103 May 20 14:26 taxonomy.dat
-rwxr-xr-x   1 vdar users    23897 May 20 14:26 Taxonomy.pm
-rwxr-xr-x   1 vdar users    20151 May 20 14:26 TRF.pm
-rwxr-xr-x   1 vdar users    14587 May 20 14:26 TRFResult.pm
drwxr-xr-x   2 vdar users     4096 May 20 14:26 util
-rwxr-xr-x   1 vdar users    41181 May 20 14:26 WUBlastSearchEngine.pm
-rwxr-xr-x   1 vdar users    35404 May 20 14:26 WUBlastXSearchEngine.pm
[vdar at capsella RepeatMasker]$ pwd
/home/vdar/RepeatMasker


But when I enter this path in my program like this

BEGIN {

        $ENV{REPEATMASKERDIR} = '/home/vdar/RepeatMasker';

 }

It gives the same error, do you still think that its not installed and I should
consult someone at campus?

Thanks!

Quoting Thomas Sharpton <sharpton at berkeley.edu>:

> 'which repeatmasker' can only find executables that are part of your
> system path  (which you can set in your .bashrc file).
>
> Did you follow these instructions when installing?
>
> http://www.repeatmasker.org/RMDownload.html
>
> If so, I'd venture a guess that the RepeatMasker executable is sitting
> in /usr/local/bin or /usr/local/RepeatMasker.
>
> Good luck,
>
> -T
>
> nisa_dar wrote:
> > I am trying to find RepeatMasker program executable by typing
> > which RepeatMasker
> > but its no where on my system, although I installed it and in my revious
> > message I have mentioned the paths of its .pm file and its directory.
> > I don't know how to find the path of what my program needs, bcs I have
> tried
> > all these paths which i mentioned in my previous message.
> > any suggestions?
> >
> >
> >
> > Florent Angly wrote:
> >
> >> The path that you set up for $ENV{REPEATMASKERDIR} should be the path to
> >> the RepeatMasker program executable, not the path to the ReapeatMasker
> >> BioPerl module.
> >> Florent
> >>
> >> nisa_dar wrote:
> >>
> >>> please see my full message and all the approaches that i have been doing
> >>> to
> >>> tell my pogram where repeat masker is...what else is correct if these are
> >>> not?
> >>>
> >>>
> >>>
> >>>
> >>> Sendu Bala-2 wrote:
> >>>
> >>>
> >>>> nisa_dar wrote:
> >>>>
> >>>>
> >>>>> ok now I have installed repeat masker, with its prerequisites as given
> >>>>> on
> >>>>> http://www.repeatmasker.org/
> >>>>> but now I am getting this error message.
> >>>>>
> >>>>> RepeatMasker program not found as  or not executable.
> >>>>>
> >>>>> what should I do?
> >>>>>
> >>>>>
> >>>> Well now you have to correct your code to tell it where you installed
> >>>> RepeatMasker:
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>>> On May 13, 2008, at 1:59 PM, nisa_dar wrote:
> >>>>>>
> >>>>>>
> >>>> [...]
> >>>>
> >>>>
> >>>>>>> BEGIN {
> >>>>>>>
> >>>>>>> 	$ENV{REPEATMASKERDIR} =
> >>>>>>> '/opt/rocks/lib/perl5/site_perl/5.8.8/Bio/Tools/';
> >>>>>>>
> >>>>>>>  }
> >>>>>>>
> >>>>>>>
> >>>> _______________________________________________
> >>>> Bioperl-l mailing list
> >>>> Bioperl-l at lists.open-bio.org
> >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>
> >>>>
> >>>>
> >>>>
> >>>
> >>>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
> >>
> >
> >
>
>
> --
> Thomas Sharpton
> PhD Candidate - UC Berkeley
> Search smarter: www.siphs.com
>
>




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